Comparative genomic and metagenomic investigations of the <i>Corynebacterium tuberculostearicum</i> species complex reveals potential mechanisms underlying associations to skin health and disease

Salamzade, Rauf; Swaney, Mary Hannah; Kalan, Lindsay

doi:10.1101/2022.08.31.506047

Cited by 2 publications

(1 citation statement)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Pneumotype SP likely overlaps with the previously identified pneumotype SP [13], although, other genera contribute to the Firmicutes-dominated population structure. Pneumotype M is predominately composed of Staphylococcus, Corynebacteria, and Cutibacterium which are genera commonly associated with the nares and skin niches [19,20]; additionally, this pneumotype is moderately abundant with microbiota associated with the human oral microbiome including Streptococcus (Figure 3). Although Cutibacterium is a prevalent contributor to pneumotype M (prevalence = 61 samples), the genus is depleted relative to pneumotype SL (FDR P < 0.001).…”

Section: Microbial Characteristics Of Pneumotypesmentioning

confidence: 99%

Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression

Sumner,

Pickens,

Huttelmaier

et al. 2024

Preprint

View full text Add to dashboard Cite

SUMMARYPneumonia and other lower respiratory tract infections are the leading contributors to global mortality of any communicable disease [1]. During normal pulmonary homeostasis, competing microbial immigration and elimination produce a transient microbiome with distinct microbial states [2–4]. Disruption of underlying ecological forces, like aspiration rate and immune tone, are hypothesized to drive microbiome dysbiosis and pneumonia progression [5–7]. However, the precise microbiome transitions that accompany clinical outcomes in severe pneumonia are unknown. Here, we leverage our unique systematic and serial bronchoscopic sampling to combine quantitative PCR and culture for bacterial biomass with 16S rRNA gene amplicon, shotgun metagenomic, and transcriptomic sequencing in patients with suspected pneumonia to distill microbial signatures of clinical outcome. These data support the presence of four distinct microbiota states—oral-like, skin-like,Staphylococcus-predominant, and mixed—each differentially associated with pneumonia subtype and responses to pneumonia therapy. Infection-specific dysbiosis, quantified relative to non-pneumonia patients, associates with bacterial biomass and elevated oral-associated microbiota. Time series analysis suggests that microbiome shifts from baseline are greater with successful pneumonia therapy, following distinct trajectories dependent on the pneumonia subtype. In summary, our results highlight the dynamic nature of the lung microbiome as it progresses through community assemblages that parallel patient prognosis. Application of a microbial ecology framework to study lower respiratory tract infections enables contextualization of the microbiome composition and gene content within clinical phenotypes. Further unveiling the ecological dynamics of the lung microbial ecosystem provides critical insights for future work toward improving pneumonia therapy.

show abstract

Section: Microbial Characteristics Of Pneumotypesmentioning

confidence: 99%

Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression

Sumner,

Pickens,

Huttelmaier

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Genomic characterization of theC. tuberculostearicumspecies complex, a ubiquitous member of the human skin microbiome

Ahmed

Joglekar

Deming

et al. 2023

Preprint

View full text Add to dashboard Cite

Corynebacteriumis a predominant genus in the skin microbiome, yet its genetic diversity on skin is incompletely characterized and lacks a comprehensive set of reference genomes. Our work aims to investigate the distribution ofCorynebacteriumspecies on the skin, as well as to expand the existing genome reference catalog to enable more complete characterization of skin metagenomes. We used V1-V3 16S rRNA gene sequencing data from 14 body sites of 23 healthy volunteers to characterizeCorynebacteriumdiversity and distribution across healthy human skin.Corynebacterium tuberculostearicumis the predominant species found on human skin and we identified two distinctC. tuberculostearicumribotypes (A & B) that can be distinguished by variation in the 16S rRNA V1-V3 sequence. One is distributed across all body sites and the other found primarily on the feet. We performed whole genome sequencing of 40C. tuberculostearicumisolates cultured from the skin of five healthy individuals across seven skin sites. We generated five closed genomes of diverseC. tuberculostearicumwhich revealed thatC. tuberculostearicumisolates are largely syntenic and carry a diversity of methylation patterns, plasmids and CRISPR/Cas systems. The pangenome ofC. tuberculostearicumis open with a core genome size of 1806 genes and a pangenome size of 5451 total genes. This expanded pangenome enabled the mapping of 24% moreC. tuberculostearicumreads from shotgun metagenomic datasets derived from skin body sites. Finally, while the genomes from this study all fall within aC. tuberculostearicumspecies complex, the ribotype B isolates may constitute a new species.

show abstract

Comparative genomic and metagenomic investigations of the Corynebacterium tuberculostearicum species complex reveals potential mechanisms underlying associations to skin health and disease

Cited by 2 publications

References 50 publications

Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression

Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression

Genomic characterization of theC. tuberculostearicumspecies complex, a ubiquitous member of the human skin microbiome

Contact Info

Product

Resources

About